Correlation clustering in R

Question

I'd like to use correlation clustering and I figure R is a good place to start.

I can present the data to R as a set of large, sparse vectors or as a table with a pre-computed dissimilarity matrix.

My questions are:

• are there existing R functions to turn this into a hierarchical cluster with agnes that uses correlation clustering?
• will I have to implement the (admittedly simple) correlation clusteringfunction by hand, if so how do I make it play well with agnes?

Answer 1

I admittedly know very little about this subject, but just to point you in a direction:

• Have you looked at the cluster package? It has very good documentation. In particular, look at help(agnes) for some suggestions. Martin Maechler (a member of the R core team) created the package and has contributed to Stack Overflow discussions before, so hopefully he'll provide an answer here.
• The hclust() function is part of the stats package. In fact, I believe that there are plans to merge hclust() and agnes().
• You may also find this page from the Bioconductor project helpful.
• Otherwise, you may have some luck looking at other packages on the CRAN Clustering, Natural Language Processing or Machine Learning views.

Answer 2

The standard approach would be one that involves cor(), hclust() and plot.hclust(). I'd highly recommend heatmap.2 from the wonderful gplots package.